The Economic Times

Black seeds inside home-canned tomatoes can look like spoilage; a harmless reaction with iron or other minerals may be responsible if the jar stayed sealed

When home-canning tomatoes, dark flecks on the seeds can appear due to interactions between minerals and plant chemicals. This phenomenon is harmless as long as jars are sealed correctly. Unfortunately, if you notice bulging lids or bad odors, it's essential to discard those jars. New canners shouldn't worry about the harmless dark spots; they are part of the process.